Charge group partitioning in biomolecular simulation

Canzar, Stefan, El-Kebir, Mohammed, Pool, Rene, Elbassioni, Khaled, Malde, Alpesh K., Mark, Alan E., Geerke, Daan P., Stougie, Leen and Klau, Gunnar W. (2012). Charge group partitioning in biomolecular simulation. In: Benny Chor, Proceedings: 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012. 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, Barcelona, Spain, (29-43). 21 - 24 April 2012. doi:10.1007/978-3-642-29627-7_3


Author Canzar, Stefan
El-Kebir, Mohammed
Pool, Rene
Elbassioni, Khaled
Malde, Alpesh K.
Mark, Alan E.
Geerke, Daan P.
Stougie, Leen
Klau, Gunnar W.
Title of paper Charge group partitioning in biomolecular simulation
Conference name 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012
Conference location Barcelona, Spain
Conference dates 21 - 24 April 2012
Proceedings title Proceedings: 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012   Check publisher's open access policy
Journal name Lecture Notes in Computer Science   Check publisher's open access policy
Place of Publication Heidelberg, Germany
Publisher Springer
Publication Year 2012
Sub-type Fully published paper
DOI 10.1007/978-3-642-29627-7_3
ISBN 9783642296260
ISSN 0302-9743
1611-3349
Editor Benny Chor
Volume 7262
Start page 29
End page 43
Total pages 15
Language eng
Formatted Abstract/Summary
Molecular simulation techniques are increasingly being used to study biomolecular systems at an atomic level. Such simulations rely on empirical force fields to represent the intermolecular interactions. There are many different force fields available|each based on a different set of assumptions and thus requiring different parametrization procedures. Recently, efforts have been made to fully automate the assignment of force-field parameters, including atomic partial charges, for novel molecules. In this work, we focus on a problem arising in the automated parametrization of molecules for use in combination with the gromos family of force fields: namely, the assignment of atoms to charge groups such that for every charge group the sum of the partial charges is ideally equal to its formal charge. In addition, charge groups are required to have size at most k. We show -hardness and give an exact algorithm capable of solving practical problem instances to provable optimality in a fraction of a second.
Keyword Charge groups
Atomic force fields
Gromos
Biomolecular simulation
Tree-decomposition
Dynamic programming
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

 
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Created: Fri, 21 Sep 2012, 20:37:55 EST by Ms Ramona Hooyer on behalf of School of Chemistry & Molecular Biosciences